SMTL ID : 9ay6.1

HIV BG505.v5.2 (N289/N241) SOSIP Env in Complex with V5 pAb from Rh.33203

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

25 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.141, N.153, S.155, Y.170, L.172, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: Q.135, S.155, F.156, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: K.234, N.246 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: E.280, N.281, N.284, K.287 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: Q.298, N.300, N.336, S.338 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.306, I.327, V.445 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: T.302, H.334, N.336, S.416, T.418, R.447 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: N.367, S.368, N.390 Ligands: NAG-BMA.10, NAG-BMA.10 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: N.267, S.296, N.451 Ligands: NAG-NAG-BMA-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.141, N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.170 NAG-NAG.13: 3 residues within 4Å: Chain C: R.197, N.202, T.203 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: E.272, N.294, E.295 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain C: N.300, N.336, V.337, S.338 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain C: N.300, T.302, H.334, N.336 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: N.367, S.368, N.390 Ligands: NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: S.296, V.449, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.396 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: N.153, Y.170, D.325 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.170 NAG-NAG.22: 2 residues within 4Å: Chain E: L.91, N.246 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain E: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain E: Q.298, I.299, N.300, V.449 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain E: N.300, T.302, N.336, S.416 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain E: N.267, S.296, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.23 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain E: T.464, N.465, S.466 Chain G: X.91 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 6 residues within 4Å: Chain E: N.390, S.392 Ligands: NAG-NAG-BMA.25, NAG-NAG-BMA.25, NAG-NAG-BMA.25, NAG-NAG-BMA.29 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.4: 11 residues within 4Å: Chain A: T.68, K.70, E.216, L.266, N.267, N.381, G.383, R.447, V.449, S.450 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.383, A:V.449, A:T.68

1 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-BMA.10: 5 residues within 4Å: Chain A: N.390, S.392 Ligands: NAG-NAG.9, NAG-NAG.9, NAG.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.390, A:S.392

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.14: 11 residues within 4Å: Chain C: K.70, E.216, P.217, V.259, L.266, N.267, N.381, G.383, V.449, S.450 Ligands: NAG-NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 10 residues within 4Å: Chain E: E.216, K.257, V.259, L.266, N.267, N.381, G.383, V.449, S.450 Ligands: NAG-NAG.28 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.383

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.25: 7 residues within 4Å: Chain E: N.367, S.368, S.369, T.376, N.390 Ligands: NAG-NAG.31, NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 4 residues within 4Å: Chain E: S.392, N.396, Q.406 Ligands: NAG-NAG.31 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.403

31 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.32: 2 residues within 4Å: Chain A: N.138, N.193 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.239, T.241, E.280 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.294, E.295 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: G.358, N.359 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.402 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.202 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: S.392, N.396 Ligands: NAG-BMA.10 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: E.92, N.93 Chain B: S.19 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: P.100, W.101, N.102 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.92, N.93 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: T.137, N.138 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: W.101, N.239, T.241, S.279 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: K.234, K.236, N.246, E.273 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.306, I.327, G.444, V.445 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.343, W.399 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: N.390, S.392 Ligands: NAG-NAG.18, NAG-NAG.18 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.281, T.283 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.359 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain D: N.102, T.104 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain E: C.136, T.137, N.138, Y.196 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain E: N.141, N.142 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: S.155, F.156, N.157 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain E: V.179, N.202 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain E: W.101, N.239, G.240, T.241, S.279 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain E: E.273, E.274, N.294, E.295, K.348 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain E: N.306, I.327, V.445 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain E: K.355, N.359 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain E: N.343, E.344, T.403, S.404 Ligand excluded by PLIP NAG.61: 5 residues within 4Å: Chain F: K.124, E.125, S.127, N.128, Y.129 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain F: N.102, T.104 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, S. et al., Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens. Sci Immunol (2025)

Release Date

2025-01-29

Peptides

Surface protein gp120: ACE
Transmembrane protein gp41: BDF
NHP Polyclonal Antibody V5 Epitope - Predicted Light Chain: G
NHP Polyclonal Antibody V5 Epitope - Predicted Heavy Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

H
L

Surface protein gp120

Transmembrane protein gp41

NHP Polyclonal Antibody V5 Epitope - Predicted Light Chain

NHP Polyclonal Antibody V5 Epitope - Predicted Heavy Chain

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